Structural Genomics @CNAG · CRG

We have contributed to the following books:


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Bibliography last updated on: 2018-04-12

There are 98 publications of article type

98.-Beekman R.,  Chapaprieta V.,  Russiñol, N.,  Vilarrasa-Blasi, R.,   Verdaguer-Dot, N.,  Martens, J.H.A.,  Duran-Ferrer, M.,  Kulis, M.,  Serra, F.,  Javierre,. B.M.,  Wingett, S.W.,  Clot, G.,  Queirós, A.C.,   Castellano, G andBlanc, J.,  Gut, M.,  Merkel, A.,  Heath, S.,  Vlasova, A.,  Ullrich, S.,  Palumbo, E.,  Enjuanes, A.,   Martín-García, D.,  Beà, S.,  Pinyol, M.,  Aymerich, M.,  Royo, R.,  Puiggros, M.,  Torrents, D.,  Datta, A.,  Lowy, E.,  Kostadima, M.,  Roller, M.,  Clarke, L.,  Flicek, P.,  Agirre, X.,  Prosper, F.,  Baumann, T.,  Delgado, J.,  López-Guillermo, A.,  Fraser, P.,  Yaspo, M-L.,  Guigó, R.,  Siebert, R.,  Marti-Renom, M.A.,  Puente, X.S.,  López-Otín, C.,  Gut, I.,  Stunnenberg, H.G.,  Campo, E. and Martin-Subero, J.I.
"The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia"
Nature Medicine (2018) in press   
97.-Kojic, A.,  Cuadrado, A.,  Koninck, A.M.,  Gomez-Lopez, G.,  Rodriguez-Corsino, M.,  Le Dily, F.,  Marti-Renom, M.A. and Losada, A.
"Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization"
Nature Structural and Molecular Biology (2018) in press   
96.-Vidal, E.,  Le Dily, F.,  Quilez, J.,  Stadhouders, R.,  Cuartero, Y.,  Graf, T.,  Marti-Renom, M.A.,  Beato, M. and Filion, G.
"OneD: increasing reproducibility of Hi-C Samples with abnormal karyotypes"
Nucleic Acids Research (2018) doi:10.1093/nar/gky0   
Journal NCBI Related BioRxiv
95.-Stadhouders, R.,  Vidal, E.,  Serra, F.,  Di Stefano, B.,  Le Dily, F.,  Quilez, J.,  Gomez, A.,  Collombet, S.,  Berenguer, C.,  Cuartero, Y.,  Hecht, J.,  Filion, G.,  Beato, M.,  Marti-Renom, M.A. and Graf, T.
"Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming."
Nature Genetics (2018) doi:10.1038/s41588-0   
Journal NCBI Related BioRxiv
94.-Spill, Y.G.,  Castillo, D. and Marti-Renom, M.A.
"Binless normalization of Hi-C data provides significant interaction and difference detection independently of resolution."
BioRxiv (2017) preprint   
93.-Di Giovanni, F.,  Di Stefano, M.,  Baù, D.,  Carey, L.B.,  Marti-Renom, M.A. and Mendoza, M.
"The spatial position of budding yeast chromosomes affects gene expression"
BioRxiv (2017) preprint   
92.-Morf, J.,  Wingett, S.W.,  Farabella, I.,  Cairns, J.,   Furlan-Magaril, M.,  Liu, X.,  Craig, F.F.,  Andrews, S.,  Marti-Renom, M.A. and Fraser, P.
"Spatial RNA proximities reveal a bipartite nuclear transcriptome and territories of differential density and transcription elongation rates."
BioRxiv (2017) preprint   
91.-Trussart, M.,  Yus, E.,  Martinez, S.,  Baù, D.,  Tahara, Y.O.,  Pengo, T.,  Kretschmer, S.,  Swoger, J.,  Miyata, M.,  Marti-Renom, M.A.,  Lluch-Senar, M. and Serrano, L.
"Defined chromosome structure in a genome-reduced bacterium, Mycoplasma pneumoniae."
Nature Communications (2017) 8 14665  
Journal NCBI Related
90.-Martínez-Jiménez, F.,  Overington, J.P.,  Al-Lazikani, B. and Marti-Renom, M.A.
"Rational design of non-resistant targeted cancer therapies."
Scientific Reports (2017) 7 46632  
Journal NCBI Related
89.-Quilez, J.,  Vidal, E.,  Le Dily, F.,  Serra, F.,  Cuartero, Y.,  Stadhouders, R.,  Graf, T.,  Marti-Renom, M.A.,  Beato, M. and Filion, G.
"Parallel sequencing lives, or what makes large sequencing projects successful"
GigaSciences (2017) 6 1-6  
Journal NCBI Related BioRxiv
88.-Goodstadt, M. and Marti-Renom, M.A.
"Challenges for visualizing three-dimensional data in genomic browsers"
FEBS Letters (2017) 591 2505–2519   
Journal NCBI Related
87.-Serra, F.,  Baù, D.,  Goodstadt, M.,  Castillo, D.,  Filion, F. and Marti-Renom, M.A.
"Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors"
PLOS Computational Biology (2017) 13(7) e1005665  
Journal NCBI Related BioRxiv
86.-Cattoni, D.I.,  Cardozo-Gizz, A.M.,  Georgieva, M.,  Di Stefano, M.,  Valeri, A.,  Chamousset, D.,  Houbron, C.,  Dejardin, S.,  Fiche, J-B.,  Marti-Renom, M.A.,  Bantignies, F.,  Cavalli, G. and Nollmann, M.
"Single-cell absolute contact probability detection reveals that chromosomes are organized by modulated stochasticity"
Nature Communications (2017) 8 1753  
Journal NCBI Related BioRxiv
85.-Le Dily, F.,  Serra, F. and Marti-Renom, M.A.
"3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data?"
WIREs Comput Mol Sci (2017) e1308  
84.-Baeza-Delgado, C.,  Von Heijne, G.,  Marti-Renom, M.A. and Mingarro, I.
"Biological insertion of computationally designed short transmembrane segments."
Scientific Reports (2016) 6 23397   
Journal NCBI Related
83.-Bogu, G.K.,   Vizan, P.,  Stanton, L.W.,  Beato, M.,  Di Croce, L. and Marti-Renom, M.A.
"Chromatin and RNA maps reveal regulatory long noncoding RNAs in mouse."
Mol Cell Biol (2016) 36 (5) 809-819  
Journal NCBI Related
82.-Martínez-Jiménez, F. and Marti-Renom, M.A.
"Should network biology be used for drug discovery?"
Expert Opinion on Drug Discovery (2016) 10.1080/17460441.201  
Journal NCBI Related
81.-Serra, F.,  Di Stefano, M.,  Spill, Y.G.,  Cuartero, Y.,  Goodstadt, M.,  Baù, D. and Marti-Renom, M.A.
"Restraint-based three-dimensional modeling of genomes and genomic domains"
FEBS Letters (2015) 589 (20) 2987–2995  
Journal NCBI Related
80.-Junier, I.,  Spill, Y.G.,   Marti-Renom, M.A.,  Beato, M. and le Dily, F.
"On the demultiplexing of chromosome capture conformation data"
FEBS Letters (2015) 589 (20) 3005–3013  
Journal NCBI Related
79.-Trussart, M.,  Serra, F.,  Baù, D.,  Junier, I.,  Serrano, L. and Marti-Renom, M.A.
"Assessing the limits of restraint-based 3D modeling of genomes and genomic domains."
Nucleic Acids Research (2015) 43 (7) 3465-3477  
Home Journal NCBI Related
78.-Sali, A.,  Berman, H.,  Schwede, T.,  Trewhella, J.,  Kleywegt, G.,  Burley, S.,  Markley, J.,  Nakamura, H.,  Adams, P.,  Bonvin, A.,  Chiu, W.,  Dal Peraro, M.,  Di Maio, F.,  Ferrin, T.,  Grünewald, K.,  Gutmanas, A.,  Henderson, R.,  Hummer, G.,  Iwasaki, K.,  Johnson, G.,  Lawson, C.,  Meiler, J.,  Marti-Renom, M.A.,  Montelione, G.,  Nilges, M.,  Nussinov, R.,  Patwardhan, A.,  Rappsilber, J.,  Read, R.,  Saibil, H.,  Schröder, G.,  Schwieters, C.,  Svergun, C.,  Topf, D.,  Ulrich, M.,  Velankar, E. and Westbrook, S.
"Outcome of the First wwPDB Hybrid / Integrative Methods Task Force Workshop"
Structure (2015) 23(7) 1156–1167  
Journal NCBI Related
77.-Belton, J-M.,  Lajoie, B.R.,  Audibert, S.,  Cantaloube, S.,  Lassadi, I.,  Goiffon, I.,  Baù, D.,  Marti-Renom, M.A.,  Bystricky, K. and Dekker, J.
"The conformation of yeast chromosome III is mating type-dependent and controlled by the recombination enhancer."
Cell Reports (2015) 13 1–13  
Journal NCBI Related
76.-Martínez-Jiménez, F. and Marti-Renom, M.A.
"Ligand-target prediction by structural network biology using nAnnoLyze."
PLOS Computational Biology (2015) 11(3) e1004157  
Home Journal NCBI Related
75.-Rebollo-Lopez, MJ.,  Lelievre, J.,  Alvarez-Gomez, D.,  Castro-Pichel, J.,  Martínez-Jiménez, F.,  Papadatos, G.,  Kumar, V.,  Colmenarejo, G.,  Mugumbate, G.,  Hurle, M.,  Barroso, V.,  Young, R.J.,  Martinez-Hoyos, M.,  Bates, R.H.,  Lopez-Roman, E.M.,  Mendoza-Losana, A.,  Brown, J.R.,  Alvarez-Ruiz, E.,  Marti-Renom, M.A.,  Overington, J.P.,  Cammack, N.,  Ballell, LL. and Barros-Aguire, D.
"Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery"
PLOS ONE (2015) 10(12) e0142293  
Journal NCBI Related
74.-Dufour, D. and Marti-Renom, M.A.
"Software for predicting the 3D structure of RNA molecules."
WIREs Comput Mol Sci (2014) 5 (1) 56–61  
73.-Le Dily, F.,  Baù, D.,  Pohl, A.,  Vicent, G.P.,  Serra, F.,  Soronellas, D.,  Castellano, G.,  Wright, R.H.G,  Ballare, C.,  Filion, G.,  Marti-Renom, M.A. and Beato, M.
"Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation"
Genes & Dev. (2014) 28 2151-2162  
Journal NCBI Related BioRxiv
72.-Martínez-Jiménez, F.,  Papadatos, G.,  Yang, L.,  Wallace, I.M.,  Kumar, V.,  Pieper, U.,  Sali, A.,  Brown, J.R.,  Overington, J.P. and Marti-Renom, M.A.
"Target prediction for an open access set of compounds active against Mycobacterium tuberculosis"
PLOS Computational Biology (2013) 9(10) e1003253  
Journal NCBI Related
71.-Baeza-Delgado, C.,  Marti-Renom, M.A. and Mingarro, I.
"Structure-based statistical analysis of transmembrane segments"
European Biophysics Journal (2013) 42 199-207  
Journal NCBI Related
70.-Köser, C.U.,  Bryant, J.M.,  Becq, J.,  Török, M.E.,  Ellington, M.J.,  Marti-Renom, M.A.,  Carmichael, A.J.,  Parkhill, J.,  Smith, G.P. and Peacock, S.J.
"Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis"
NEJM (2013) 369 290-292  
Journal NCBI Related
This article has been highlighted in Nature here and here.
69.-Kemena, C.,  Bussotti, G.,  Capriotti, E.,  Marti-Renom, M.A. and Notredame, C
"Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package"
Bioinformatics (2013) 29 1112-1119  
Journal NCBI Related
68.-López-Pelegrín, M.,  Cerdà-Costa, N.,  Martínez-Jiménez, F.,  Cintas, A.,  Canals, A.,  Peinado, J.R.,  Marti-Renom, M.A.,  López-Otín, C.,   Arolas, J.L. and Gomis-Rüth, F.X.
"A novel family of soluble minimal scaffolds provides structural insight into the catalytic domains of integral-membrane metallopeptidases."
JBC (2013) 288 21279–21294  
Journal NCBI Related
67.-Dekker, J.,  Marti-Renom, M.A. and Mirny, L.A.
"Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data"
Nature Reviews Genetics (2013) 14 390–403  
Journal NCBI Related
66.-Bañó-Polo, M.,  Baeza-Delgado, C.,  Orzáez, M.,  Marti-Renom, M.A.,  Abad, C. and Mingarro, I.
"Polar/Ionizable residues in transmembrane segments: effects on helix-helix packing."
PLoS ONE (2012) 7 e44263  
Journal NCBI Related
65.-Baù, D. and Marti-Renom, M.A.
"Genome structure determination via 3C-based data integration by the Integrative Modeling Platform"
Methods (2012) 58 300–306  
Journal NCBI Related
64.-Marti-Renom, M.A. and Mirny L.
"Bridging the resolution gap in structural modeling of 3D genome organization"
PLoS Computational Biology (2011) 7 e1002125  
Journal NCBI Related
63.-Feuerriegel, I.,  Köser, C.,  Baù, D.,  Rüsch-Gerdes, S.,  Summers, D.,  Archer, J.,  Marti-Renom, M.A. and Niemann, S.
"Impact of fgd1 and ddn diversity in Mycobacterium tuberculosis complex on in vitro susceptibility to PA-824"
Antimicrobial Agents and Chemotherapy (2011) 55 5718-5722  
Journal NCBI Related
62.-Umbarger, M.A.,  Toro, E.,  Wright, M.A.,  Porreca, G.J.,  Baù, D.,  Hong, S-H.,  Fero, M.J.,  Zhu, J.,  Marti-Renom, M.A.,  McAdams, J.H.,  Shapiro, L.,  Dekker, J. and Church, G.M.
"The three-dimensional architecture of a bacterial genome and Its alteration by genetic perturbation"
Molecular Cell (2011) 44 252–264  
Journal NCBI Related Fac1000
This article has been highlighted in a Journal Club at the NRMCB and in a News & Views at NRM.
61.-Martínez-Gil, L. ,  Saurí, A.,  Marti-Renom, M.A. and Mingarro, I
"Membrane protein integration into the ER"
FEBS Journal (2011) 278 3846–3858  
Journal NCBI Related
60.-Capriotti, E.,  Norambuena, T,  Marti-Renom, M.A. and Melo, F.
"All-atom knowledge-based potential for RNA structure prediction and assessment"
Bioinformatics (2011) 27 1086-1093  
Journal NCBI Related
59.-Sanyal, A.,  Baù, D.,  Marti-Renom, M.A. and Dekker, J.
"Chromatin globules: a common motif of higher-order chromosome structure?"
Current Opinion in Cell Biology (2011) 23 325–33  
Journal NCBI Related
58.-Bañó-Polo, M. ,  Baldin, F.,  Tamborero, S.,  Marti-Renom, M.A. and Mingarro, I
"N-Glycosylation efficiency is determined by the distance to the C-terminus and the amino acid preceding an Asn-Ser-Thr sequon."
Protein Science (2011) 20 179–186  
Journal NCBI Related
57.-Baù, D. and Marti-Renom, M.A.
"Structure determination of genomic domains by satisfaction of spatial restraints"
Chromosome Research (2011) 19 (1) 25  
Journal NCBI Related
56.-Baù, D.,  Sanyal, A.,  Lajoie, B.R.,  Capriotti, E.,   Byron, M.,   Lawrence J.B.,  Dekker, J. and Marti-Renom, M.A.
"The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules"
Nature Structural and Molecular Biology (2011) 18 107-114  
Journal NCBI Related This article has been highlighted in a Technology Feature at the Nature Journal.
55.-Capriotti, E. and Marti-Renom, M.A.
"Quantifying the relationship between sequence and three-dimensional structure conservation in RNA"
BMC Bioinformatics (2010) 11 322  
Journal NCBI Related
54.-Madhusudhan, MS.,  Webb, B.,  Marti-Renom, M.A.,  Eswar, N. and  Sali, A.
"Alignment of multiple protein structures based on sequence and structure features."
PEDS (2009) 22 569-574   
Home Journal NCBI Related
53.-Capriotti, E. and Marti-Renom, M.A.
"SARA: a server for function annotation of RNA structures"
Nucleic Acids Research (2009) 37 W260-5  
Home Journal NCBI Related
52.-Fornes, O.,  Aragues, R.,  Espadaler, J.,  Marti-Renom, M.A.,  Sali, A. and Oliva, B.
"ModLink+: Improving fold recognition by using protein-protein interactions"
Bioinformatics (2009) 25 1506-12  
Home Journal NCBI Related
51.-Orti, L.,   Carbajo, R.J.,   Pieper, U.,  Eswar, N.,  Maurer, S.M.,  Rai, A.K.,  Taylor, G.,  Todd, M.H.,  Pineda-Lucena, A.,  Sali, A. and Marti-Renom, M.A.
"A kernel for open source drug discovery in tropical diseases"
PLoS Neglected Tropical Diseases (2009) 3 e18  
Home Journal NCBI Related
50.-Orti, L.,   Carbajo, R.J.,   Pieper, U.,  Eswar, N.,  Maurer, S.M.,  Rai, A.K.,  Taylor, G.,  Todd, M.H.,  Pineda-Lucena, A.,  Sali, A. and Marti-Renom, M.A.
"A kernel for the Tropical Disease Initiative"
Nature Biotechnology (2009) 27 320-321  
Home Journal NCBI Related This is a Correspondence to the Editor.
49.-Pieper, U.,  Eswar, N.,  Webb, B.M.,  Eramian, D.,  Kelly, L.,  Barkan, D.T.,  Carter, H.,  Mankoo, P.,  Karchin, R.,  Marti-Renom, M.A.,  Davis, F.P. and Sali, A.
"MODBASE, a database of annotated comparative protein structure models, and associated resources."
Nucleic Acids Research (2009) 37 D347-D354  
Home Journal NCBI Related
48.-Espadaler, J.,  Eswar, N.,  Querol, E.,  Aviles, F.X.,  Sali, A.,  Marti-Renom, M.A. and Oliva, B.
"Prediction of enzyme function by combining sequence similarity and protein interactions"
BMC Bioinformatics (2008) 9(1) 249  
Journal NCBI Related
47.-Panjkovich, A.,  Melo, F. and Marti-Renom, M.A.
"Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs"
Genome Biology (2008) 9 R68  
Journal NCBI Related
46.-Capriotti, E. and Marti-Renom, M.A.
"Computational RNA structure prediction "
Current Bioinformatics (2008) 3 (1) 32-45  
Home Journal
45.-Capriotti, E.,  Arbiza, L.,  Casadio, R.,  Dopazo, J.,  Dopazo, H. and Marti-Renom, M.A.
"The use of estimated evolutionary strength at the codon level improves the prediction of disease related protein mutations in human."
Human Mutation (2008) 29 (1) 198-204  
Home Journal NCBI Related
44.-Capriotti, E. and Marti-Renom, M.A.
"RNA structure alignment by a unit-vector approach"
Bioinformatics (2008) 24 i112-i118  
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43.-Eswar, N.,  Webb, B.,  Marti-Renom, M.A. ,  Madhusudhan, M.S.,  Eramian, D.,  Shen, M-Y.,  Pieper, U. and Sali A.
"Comparative Protein Structure Modeling Using MODELLER. "
Current Protocols in Protein Science (2007) 2.9 (Nov 2007) 2.9.1-2.9.31  
Journal NCBI Related pdf This is an updated and revised version of the CPPS unit published in Nov. 2002
42.-Marti-Renom, M.A.,   Rossi, A.,  Al-Shahrour, F.,   Davis, F.,  Pieper, U.,  Dopazo, J. and Sali, A.
"The AnnoLite and AnnoLyze programs for comparative annotation of protein structures"
BMC Bioinformatics (2007) 8 (Suppl 4) S4  
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41.-Stanley, W.A.,  Fodor, K.,   Marti-Renom, M.A.,  Schliebs, W. and Wilmanns, M.
"Protein translocation into peroxisomes by ring-shaped import receptors"
FEBS Letters (2007) 581 4795-802  
Journal NCBI Related
40.-Marti-Renom, M.A.,  Pieper, U.,  Madhusudhan, M.S.,  Rossi, A.,  Eswar, N.,  Davis, F.P.,  Al-Shahrour, F.,  Dopazo, J. and  Sali A.
"DBAli tools: mining the protein structure space"
Nucleic Acids Research (2007) 35 W393-W397  
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39.-Aragues, R.,   Sali, A.,  Bonet, J.,  Marti-Renom, M.A. and Oliva, B.
"Characterization of protein hubs by inferring interacting motifs from protein interactions"
PLoS Computational Biology (2007) 3(9) e178  
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38.-Melo, F. and Marti-Renom, M.A.
"Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets"
Proteins (2006) 63 986-995  
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37.-Kepler, T.,  Marti-Renom, M.A.,  Maurer, S.M.,  Rai A.K.,  Taylor, G. and Todd, M.H
"Open Source Research - The power of Us"
Aust. J. Chem. (2006) 59 291-294  
36.-Eswar, N.,  Webb, B.,  Marti-Renom, M.A. ,  Madhusudhan, M.S.,  Eramian, D.,  Shen, M-Y.,  Pieper, U. and Sali A.
"Comparative Protein Structure Modeling with MODELLER"
Current Protocols in Bioinformatics (2006) 5.6 (Dec 2006) 5.6.1-5.6.30  
Journal NCBI Related pdf This is an updated and revised version of the CPBI unit published in Nov 2003
35.-Topf, M.,  Baker, ML.,  Marti-Renom, MA.,  Chiu, W and Sali, A
"Structure characterization of assembly components by iterative comparative modeling and cryoEM density fitting"
J. Mol. Biol. (2006) 357(5) 1655-68  
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34.-Pieper, U.,  Eswar, N.,   Davis, F.,   Braberg, H.,  Madhusudhan, M.S.,,  Rossi, A.,  Marti-Renom, M.A.,  Karchin, R.,  Webb, B.,  Eramian, D.,  Shen, M-Y.,  Kelly, L.,  Melo, F. and Sali, A.
"MODBASE, a database of annotated comparative protein structure models, and associated resources"
Nucleic Acids Research (2006) 34 D291-295  
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33.-Madhusudhan, MS.,  Marti-Renom, MA.,  Sanchez, R. and Sali, A.
"Variable gap penalty for protein sequence-structure alignment"
PEDS (2006) 19 129-133  
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32.-Rossi, A.,  Marti-Renom, M.A. and Sali, A.
"Localization of binding sites in protein structures by optimization of a composite scoring function"
Protein Science (2006) 15 2366-2380  
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31.-Eramian, D.,  Shen, M-Y.,  Devos, D.,  Melo, F.,  Sali, A. and Marti-Renom, M.A.
"A composite score for predicting errors in protein structure models"
Protein Science (2006) 15 1653-1666  
Journal NCBI Related
30.-McMahon, S.A.,  Miller, J.L.,  Lawton, J.A.,  Kerkow, D.E.,  Hodes, A.,  Marti-Renom, M.A.,  Doulatov, S.,  Eswar, N.,  Sali, A.,  Miller, J.F. and Ghosh, P.
"The C-type lectin fold as a scaffold for massive sequence variation"
Nature Structural and Molecular Biology (2005) 12 886-892  
Journal NCBI Related Fac1000 recommended
29.-Espadaler, J.,  Aragues, R.,  Eswar, N.,  Marti-Renom, M.A.,  Querol, E.,  Aviles, F.X.,  Sali, A. and Oliva, B.
"Detecting remote homology by sequence similarity and protein-protein interactions."
Proc. Natl. Acad. Sci. USA. (2005) 102 7151-7156  
Journal NCBI Related
28.-Mirkovic, N.,  Marti-Renom, M.A.,  Weber, B.L.,  Sali, A. and Monteiro, A.N.A.
"Structure-based assessment of missence mutations in human BRCA1: Implications for breast and ovarian cancer predisposition."
Cancer Research (2004) 64 3790-3797  
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27.-Pieper, U.,  Eswar, N.,  Braberg, H.,  Madhusudhan, MS.,  Davis, FP.,  Stuart, AC.,  Mirkovic, N.,  Rossi, A.,  Marti-Renom, MA.,  Fiser, A.,  Webb, B.,  Greenblatt, D.,  Huang, CC.,  Ferrin, TE. and Sali, A.
"MODBASE, a database of annotated comparative protein structure models, and associated resources."
Nucleic Acids Res (2004) 32 D217-22  
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26.-Marti-Renom, M.A.,  Madhusudhan, M.S. and Sali, A.
"Alignment of protein sequences by their profiles"
Protein Science (2004) 13 1071-1087  
Journal NCBI Related
25.-Marti-Renom, M.A.,   Fiser, A.,  Madhusudhan, M.S.,  John, B.,  Stuart, A.,  Eswar, N.,  Pieper, P.,  Shen, MY. and Sali, A.
"Modeling protein structure from its sequence"
Current Protocols in Bioinformatics. Ed: John Wiley & Sons, Inc. (2003) 5.1 (Nov 2003) 5.1.1-5.1.22  
Journal pdf This is an updated and revised version of the original CPBI unit published in Jan 2003
24.-Marti-Renom, M.A.
"Protein Structure Modeling for Structural Genomics"
Business Briefing: Future Drug Discovery (2003) June 59-63  
Journal pdf
23.-Marti-Renom, M.A.,  Yercovich, B. and Sali, A.
"Modeling protein structure from its sequence."
Current Protocols in Bioinformatics. Ed: John Wiley & Sons, Inc. (2003) 5.1 (Jan 2003) 5.1.1-5.1.22  
Journal pdf
22.-Koh, I-Y. Y. ,  Eyrich, V.A.,  Marti-Renom, M.A.,  Przybylski, D.,  Madhusudhan, M.S.,  Narayanan, E.,  Graña, O.,  Pazos, F.,  Valencia, A.,  Sali, A. and Rost, B.
"EVA: evaluation of protein structure prediction servers"
Nucleic Acids Research (2003) 31 3311-3315  
Home Journal NCBI Related
21.-Narayanan, E.,  John, B.,  Mirkovic, N.,  Fiser, A.,  Ilyin, V.,  Pieper, U.,  Stuart, A.C.,  Marti-Renom, M.A.,  Madhusudhan, M.S.,  Yerkovich, B. and Sali A.
"Tools for comparative protein structure modeling and analysis"
Nucleic Acids Research (2003) 31 3375-3380.  
Home Journal NCBI Related
20.-Ilyin, VA.,  Pieper, U.,  Stuart, AC.,  Marti-Renom, MA.,  McMahan, L. and Sali, A.
"ModView, visualization of multiple protein sequences and structures."
Bioinformatics (2003) 19 165-6  
home journal MedLine related pdf
19.-Iverson, GM.,  Reddel, S.,  Victoria, EJ.,  Cockerill, KA.,  Wang, YX.,  Marti-Renom, MA.,  Sali, A.,  Marquis, DM.,  Krilis, SA. and Linnik, MD.
"Use of Single Point Mutations in Domain I of beta(2)-Glycoprotein I to Determine Fine Antigenic Specificity of Antiphospholipid Autoantibodies."
J Immunol (2002) 169 7097-7103  
Journal NCBI Related pdf
18.-Martí-Renom, M.A.,  Madhusudhan, M.S.,  Fiser, A.,  Rost, B. and Sali, A.
"Reliability of assessment of protein structure prediction methods"
Structure (2002) 10 435--440  
journal NCBI Related pdf Fac1000 recommended
17.-Sali, A.,  Martí-Renom, M.A.,  Madhusudhan, M.S.,  Fiser, A. and Rost, B.
"Reply To Moult et al."
Structure (2002) 10 292--293  
Journal pdf
16.-Martí-Renom, M.A.,  Yercovich, B. and Sali, A.
"Comparative Protein Structure Prediction"
Current Protocols in Protein Science (2002) 1 2.9.1-2.9.22,  
Journal pdf
15.-Eyrich, V.,  Martí-Renom, M.A.,  Przybylski, D.,  Fiser, A.,  Madhusudhan, M.S.,  Pazos, F.,  Valencia, A.,  Sali, A. and Rost, B.
"EVA: continuous automatic evaluation of protein structure prediction servers."
Bioinformatics (2001) 17 1242-1243  
Home Journal NCBI Related
14.-Marti-Renom, MA.,  Ilyin, VA. and Sali, A.
"DBAli: a database of protein structure alignments."
Bioinformatics (2001) 17 746-7  
Home Journal NCBI Related
13.-Mas, JM.,  Aloy, P.,   Martí-Renom, M.A.,  Oliva, B.,  de Llorens, R.,  Aviles, FX. and Querol, E.
"Classification of protein disulphide-bridge topologies."
J Comput Aided Mol Des (2001) 15 477-87  
Journal NCBI Related
12.-Sánchez, R.,  Pieper, U.,  Melo, F.,  Eswar, N.,  Martí-Renom, M.A.,  Madhusudhan, M.S.,  Mirkovic, N. and Sali, A.
"Protein structure modeling for structural genomics"
Nat Struct Biol (2000) 7 Suppl 986--90  
Journal NCBI Related pdf
11.-Martí-Renom, M.A.,  Stote, R.H.,  Querol, E.,  Avilés, F.X. and Karplus, M.
"Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints."
Proteins (2000) 40 482--493  
Journal NCBI Related pdf
10.-Martí-Renom, M.A.,  Stuart, A.,  Fiser, A.,  Sánchez, R.,  Melo, F. and Sali, A.
"Comparative protein structure modeling of genes and genomes."
Annu Rev Biophys Biomol Struct (2000) 29 291--325  
Journal NCBI Related pdf
9.-Serra-Hartmann, X.,  Rebordosa, X.,  Piñol, J.,  Querol, E. and Martí-Renom, M.A.
"ASAP analysis of peptide composition."
Bioinformatics (2000) 16 1153--1154  
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8.-Aloy, P.,  Mas, J.M.,  Martí-Renom, M.A.,  Querol, E.,  Avilés, F.X. and Oliva, B.
"Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: application to the human procarboxypeptidase A2."
J Comput Aided Mol Des (2000) 14 83--92  
Journal NCBI Related pdf
7.-Liedtke, W.,  Choe, Y.,  Martí-Renom, M.A.,  Bell, A.M.,  Denis, C.S.,  Sali, A.,  Hudspeth, A.J.,  Friedman, J.M. and Heller, S.
"Vanilloid receptor-related osmotically activated channel (VR-OAC), a candidate vertebrate osmoreceptor"
Cell (2000) 103 525--35  
Journal NCBI Related pdf
6.-Martí-Renom, M.A.
"ASAP, web server for analysis of peptide composition"
CCP11 Newsletters (1999) 9 2-3  
Home Journal PDF
5.-Martí-Renom, M.A.,  Stote, R.H.,  Querol, E.,  Avilés, F.X. and Karplus, M.
"Refolding of potato carboxypeptidase inhibitor by molecular dynamics simulations with disulfide bond constraints"
J Mol Biol (1998) 284 145--72  
Journal NCBI Related pdf
4.-Mas, J.M.,  Aloy, P.,  Martí-Renom, M.A.,  Oliva, B.,  Blanco-Aparicio, C.,  Molina, M.A.,  de, Llorens, R.,  Querol, E. and Avilés, F.X.
"Protein similarities beyond disulphide bridge topology"
J Mol Biol (1998) 284 541--8  
Journal NCBI Related pdf
3.-Stote ,R.H.,  Martí-Renom, M.A.,  Querol, E.,  Aviles, F.X. and Karplus, M.
"Molecular dynamics simulations of the unfolding and refolding of potato carboxypeptidase inhibitor"
ABSTR PAP AM CHEM S (1998) 216 U272  
2.-Martí-Renom, M.A.,  Mas, J.M.,  Aloy, P.,  Querol, E.,  Avilés, F.X. and Oliva, B.
"Statistical Analysis of the Loop-geometry on a Non-redundant Database of Proteins"
J Mol Model (1998) 11 347--354  
journal pdf
1.-Martí-Renom, M.A.,  Mas, J.M.,  Oliva, B.,  Querol, E. and Avilés, F.X.
"Effects of counter-ions and volume on the simulated dynamics of solvated proteins. Application to the activation domain of procarboxypeptidase B"
Protein Eng (1998) 11 881--90  
Journal NCBI Related pdf

There are 7 publications of book type

7.-Dufour, D. and Marti-Renom, M.A.
"Modeling of RNA sequences"
(2013) Springer Edition 2013 p1566-1569  
Journal Amazon
6.-Dufour, D.,  Capriotti, E. and Marti-Renom, M.A.
"Computational methods for RNA structure prediction and analysis."
(2013) PanStanford Publishing 1st edition   
5.-Marti-Renom, M.A.,  Capriotti, E.,  Shindyalov, I. and Bourne, P.
"Structural Comparison and Alignment. In: Structural Bioinformatics. "
(2009) Wiley-Blackwell, New Jersey. USA. 2nd Edition   
4.-Engelen, S. and Marti-Renom, M.A.
"Open source drug discovery: The Tropical Disease Initiative. In: In Sickness and in Health. The Future of Medicine: Added Value and Global Access."
(2009) VUBPRESS, Brussels, Belgium   
3.-Capriotti, E. and Marti-Renom, M.A.
"Assessment of protein structure predictions. In: Computational Structural Biology. "
(2008) World Scientific Publishing Company. New Jersey. USA.   
2.-Madhusudhan, M.S.,  Marti-Renom, M.A.,   Eswar, N.,  John, B,  Pieper, U.,   Karchin, R.,  Shen, M-Y and Sali, A
"Comparative protein structure prediction. In: The Proteomics Protocols Handbook."
(2005) Humana Press Inc. Totowa, NJ. 835-864  
Journal Amazon
1.-Barbadilla, A.,  Naveira, H.,  Santos, M.,  Martí-Renom, M.A. and Peris, F.
"Introducción al BMDP en VAX/VMS"
(1992) UAB, Bellaterra, Spain   
Practices book for Biostatistics at 3rd grade in Biology studies

There are 6 publications of phdthesis type

6.-Baeza-Delgado, C.,  Marti-Renom, M.A. and Mingarro, I.
"On the design of optimally inserted transmembrane helices"
(2017) Valencia, Spain   
5.-Bogu, G.K.,  Marti-Renom, M.A. and Guigó, R.
"Understanding the transcriptional landscape of non-coding genome (lncRNAs and repetitive elements) in mammals"
(2017) Barcelona, Spain   
4.-di Giovanni, F.,  Marti-Renom, M.A. and Mendoza, M.
"The impact of chromosome positioning in nuclear functions"
(2016) Barcelona, Spain   
3.-Martínez-Jiménez, F. and Marti-Renom, M.A.
"Structural study of the therapeutic potential of protein-ligand interactions"
(2016) Barcelona, Spain   
2.-Trussart, M.,  Marti-Renom, M.A. and Serrano, L.
"Structure determination of Mycoplasma pneumoniae genome"
(2015) Barcelona, Spain   
1.-Martí-Renom, M.A.
"On the Unfolding and Refolding of Potato Carboxypeptidase Inhibitor"
(1999) Bellaterra, Spain   
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